Volume 15, Issue 1, Pages 75-83 (January 2007) DNA Recognition Mechanism of the ONECUT Homeodomain of Transcription Factor HNF-6  Daisuke Iyaguchi, Min Yao, Nobuhisa Watanabe, Jun Nishihira, Isao Tanaka  Structure  Volume 15, Issue 1, Pages 75-83 (January 2007) DOI: 10.1016/j.str.2006.11.004 Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 1 Structural Overview of the DNA-Binding Domain Complexed with DNA (A) An overview of the HNF-6-DNA complex. The cut domain and the homeodomain of HNF-6 are shown in light blue and yellow, respectively. Helices 1–9 are labeled. (B) Two overviews of the Oct-1-DNA complex related by 70° rotation about the axis parallel to the helical axis of the DNA showing that the POU domain (left figure) and the homeodomain (right figure) can be superimposed with the cut domain and the homeodomain of (A). The POU-specific domain and the homeodomain of Oct-1 are shown in green and orange, respectively. (C) HNF-6 and Oct-1 are shown in the same colors as in (A) and (B). HNF-6 (left) and Oct-1 (right) are related by 90° rotation about the horizontal axis to (A) and the right view of (B), respectively. Structure 2007 15, 75-83DOI: (10.1016/j.str.2006.11.004) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 2 Sequence of the DNA Duplex Used for Cocrystallization and of the DNA-Binding Domain of HNF-6 (A) DNA duplex used for cocrystallization. Base pairs 1–13 are from the rat TTR promoter. The 5′-half subsite and the 3′-half subsite are boxed. Asterisks indicate the positions replaced by 5-bromouridines for phasing. (B) DNA duplex used for cocrystallization of Oct-1. The ATGC subsite (5′ half) and the AAAT subsite (3′ half) of an octamer site are boxed (Klemm et al., 1994). (C) The amino acid sequence of the DNA-binding domain of HNF-6 is shown; the single-letter amino acid code is used. The regions corresponding to the cut domain and the homeodomain are boxed, and the linker segment is labeled. Helices seen in the crystal structure are indicated below the sequence. Structure 2007 15, 75-83DOI: (10.1016/j.str.2006.11.004) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 3 Structural Comparison of the Cut Domain and the POU-Specific Domain (A) Structural comparison of the cut domains of the DNA-bound and DNA-free structures. The cut domain of the DNA-bound crystal structure is shown in light blue, and that of the DNA-free NMR structure is shown in pink. Helices 1–6 of the cut domain are labeled. (B) Structural comparison of the POU-specific domains of the DNA-bound and DNA-free structures. The POU-specific domain of the DNA-bound crystal structure of Oct-1 is shown in green, and that of the DNA-free NMR structure is shown in red. (C) Structural comparison of the cut domain and the POU-specific domain. The cut domain of the DNA-bound crystal structure of HNF-6 is shown in light blue. The POU-specific domain of the DNA-bound crystal structure of Oct-1 is shown in green. Helices 1–6 of the cut domain are labeled. Structure 2007 15, 75-83DOI: (10.1016/j.str.2006.11.004) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 4 Sequence Comparison of the Cut Domain of HNF-6 and the POU-Specific Domain of Oct-1 Residue numbers and secondary structures in the DNA-binding structure of the cut domain and the POU-specific domain are shown above and below each sequence, respectively. Residues involved in the formation of the hydrophobic core are shown in red. Residues hydrogen bonding to backbone atoms and bases of the DNA are shown in light blue and green, respectively. Residues hydrogen bonding to both backbone atoms and bases are shown in purple. Residues identical between the two domains are boxed. Structure 2007 15, 75-83DOI: (10.1016/j.str.2006.11.004) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 5 Protein-DNA Contacts Schematic diagram of protein-DNA contacts. Residues from the cut domain are shown in light blue, and the homeodomain is shown in yellow. The bases, phosphates, and sugars contacted by each domain are indicated in the corresponding colors. The bases contacted by both domains are shown in red. Solid black lines indicate hydrogen bonds. van der Waals interactions are indicated as dashed blue lines. Water molecules are shown as green spheres. Structure 2007 15, 75-83DOI: (10.1016/j.str.2006.11.004) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 6 Detailed View of the Homeodomain-DNA Interactions Interactions of Asn-143, Met-146, Asn-147, and Arg-150 with DNA are shown. Dashed red lines indicate hydrogen bonds. van der Waals interactions are indicated as dashed blue lines. Water molecules are shown as green spheres. Residue numbers and base numbers are labeled. Structure 2007 15, 75-83DOI: (10.1016/j.str.2006.11.004) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 7 Conformational Change in DNA Backbone structures of DNA complexed with HNF-6 and Oct-1 are shown. HNF-6 (left) and Oct-1 (right) are shown in the same colors as in Figure 1. Structure 2007 15, 75-83DOI: (10.1016/j.str.2006.11.004) Copyright © 2007 Elsevier Ltd Terms and Conditions